The objective of Project CyberCell is to develop an accurate simulation of a living cell within the virtual environment of a computer, one that can be manipulated at different levels of molecular resolution, and, that can respond, adapt and evolve to exploit this virtual environment. Project CyberCell has selected the bacterium E. coli as its model. As the project evolves, this model has the potential to generate concepts and technology for extending cellular simulation to more complicated cell types and eventually multi-cellular organisms.

Project CyberCell is Canada’s contribution to an escalating international effort to simulate living systems computationally. We are consortium of researchers from Canadian universities and research institutions that is headquartered in Alberta. Project CyberCell has adopted a direction that is complementary to related initiatives found elsewhere. We are committed to integrating our activities meaningfully and productively with the international community by an open and full exchange of ideas and information.

New device joins battle against disease

Looking much like a set of computers with protuding tubes and flasks, a $500,000 spectrometer that promises to advance cell research was shown off at the University of Alberta on Monday.

The spectrometer identifies hundreds of proteins in a cell and could lead to develoment of new drugs for diseases such as cancer, heart and respiratory diseases, university officials said.

“The fastest way to get to the cause of a disease, or to figure out what new kinds of drugs have to be designed to combat the disease is through the proteins,” said Michael Ellison, executive director of the university’s Institute for Biomolecular Design.

“The research could also be used for cell research in fields such as forestry, or agriculture such as the development of grains that are more resistant to diseases,” Ellison said.

The spectrometer and its associated laboratory are the largest in Western Canada. They were displayed during the official launch of the Alberta Network for Proteomics Innovation.

Proteomics is the study of proteins. The network will link scientists and researchers of Alberta, Calgary and Lethbridge.

The network, operating unofficially for about two years, now has $16.2 million in funding from the Alberta and Federal governments: the Alberta Science and Research Authority contributed $10 million with the balance coming from the federal Western Economic Diversification Department.

The spectrometer is one of the first pieces of equipment funded by the network, according to U of A officials.

Standing in front of a computer screen, Ellison pointed to black spots and splotches that scientists have identified as proteins within an E. Coli cell.

“The cell — a variation of which is best known for its deadly effects in the water contamination incident at Walkerton, Ont. — is being studied because it’s one of the simler cells, with 4,000 different kinds of proteins in it,” Ellison said. Human cells, by contrast, contain about 50,000 proteins.

“Researchers hope to use the spectrometer to study how different drugs and chemicals affect the various proteins and thus target the effects of drugs more carefully for desired effects,” Ellison said.

“Imagine being able to see what the drugs do in terms of side-effects on the cell and then trying to optimize the positive effects.” Ellison said. The machine cold be used for that kind of research as early as six months from now.

“The spectrometer is also being used to develop a “virtual cell” upon which various drugs and chemicals can be tested, but its development is three to five years away,” Ellison said.

Computer simulation of cells may replace laboratory work

Is the laboratory’s ubiquitous petri dish about to be displaced by a computer simulation so sophisticated it can replicate the complete life cycle of a single cell?

And will the appearance of a four-dimensional “virtual cell” turn the current hit-or-miss world of new drug development into something that closer to a predictable science?

The answer to both questions seems to be a guarded “yes” according to researchers involved with a new Canadian-led effort to simulate in a computer the E. coli bacteria’s life history.

Michael Ellison, a biologist at the University of Alberta, told a session of the BIO 2002 conference yesterday that his group believes that in three years they will have a rough working model of such a computer-generated life form.

“The implication of being able to simulate life on a computer is that you can do research and make discoveries far more quickly and cheaply and efficiently than the work done now,” the University of Alberta biochemist who heads up what is known as Project Cybercell told reporters.

Currently, one of the big stumbling blocks for drug development is the haphazard way new drugs are discovered. In the main, companies simply test compounds on cells or animals to see if there is any discernible effect. If they find a potentially useful reaction, they manipulate the drug in a number of ways. They then go through the same generalized testing again to see if any of their manipulations has increased the potency of the chemical they are studying.

A virtual cell holds out the possibility of seeing how a potentially beneficial chemical affects an entire cell in a few minutes. The “whole” approach is required because biologists now suspect that how a cell reacts to a disease or a drug is not a function of a single gene or protein being turned on or off, but reflects an essential change in the way the total cell functions.

Cybercell presents at Bio 2002

Project Cybercell presented itself to the global biotech community at the Bio 2002 meeting of 15,600 particpants at the Metro Toronto Convention Centre. Dr. Mike Ellison hosted the 90 minute session which featured presentations by Dr. Joel Weiner on challenges in the biochemistry of the Cybercell; Dr. David Wishart on Cyberinformatics; the Cybercell databases; Dr. Frank Meyer of Computer Modelling Group on 4-d simulations of the Cybercell and by Colin Hill of GNS on the genetic circuitry of the Cybercell.

The gathered crowd showed great interest in both the content of the presentations and the concept of the Cybercell in a lively questions and answer session after the presentations. The media was in attendance and their interest generated an article in the Globe and Mail as well as a series of interviews on CBC radio featuring Dr. Ellison.

Dr. Ellison will also be presenting Project Cybercell on Discovery TV this fall.

CyberCell awarded $4.7m from Alberta Government

…Project CyberCell, a collaborative effort involving the universities of Alberta, Calgary and Lethbridge, was given $4.7 million to build a cell on a computer.

“When complete, the cell will be useful in a number of ways,” said Joel Weiner, the project’s scientific director.

“We could propose how a drug will act or how a cell will function in a particular environment,” he said, adding researchers will be able to determine the effects mutations have on a cell.

Weiner said CyberCell researchers are currently collecting data. And, over the next few years, they will attempt to complete the first step of the project, computer modelling E. Coli bacteria cell.

Weiner said the project will provide a number of high-tech jobs and attract graduate students to the university, which he considers a world leader in the biology field. “There are a number of projects in different countries, and we’re clearly in front,” he said, estimating it will be about 10 years before a human cell is replicated in the computer.

“All we have is a parts list, and we have no idea how the parts go together. It’s like getting an IKEA kit without the schematic, and you have a whole bunch of different parts sitting in front of you,” he said.

We’re trying to figure out from the parts how to put this thing together, and build it bit by bit until we have a cell.”

CyberCell receives $1 million for project development

A funding partnership between the Government of Alberta, the federal Ministry of Western Economic Diversification and Genome Prairie recently awarded Project CyberCell with $1 million to develop proof of concept for the virtual cell in anticipation of its application to Genome Canada for additional funding later this year.

Project CyberCell has secured favourable opinions from our trademark agents for the protection of CyberCell as trademarked property. We have made application in both Canada (priority date 16 July 2001) and the United States (Priority Date 6 August 2001) and now await official notification.

A Forum for the Virtual Cell

On 3-7 Aug., 2002, Edmonton will host International Society for Computational Biology (ISMB) the world’s largest conference on computational biology. For more information about this conference, see http://www.cs.ualberta.ca/~ismb02/. For information about the sponsoring organization, The International Society for Computational Biology, see http://www.iscb.org/

A Harmonic Convergence: CyberCell and Alberta’s Oilpatch

….As one of the more surprising examples of haut tech conversion, Project CyberCell has joined forces with the Computer Modelling Group Ltd. of Calgary to develop a four dimensional simulation platform of a virtual living cell. CMG has been involved in modelling, simulation and visualization of complex processes associated with oil and gas recovery for the past 24 years. Dr. Mike Ellison, director of Project Cybercell notes, ” CMG’s abilty to accurately predict in space and time, the complex chemical behaviour of solids, gases and liquid within a complicated geological setting, makes its software ideally suited to cellular simulation. As academics,our partnership with CMG has taught us two valuable lessons. Speed counts but open-mindedness is equally important- Collaborate or die!” A protoype of their virtual cell should be ready later this year.

Project Cybercell defines convergence

Johanna Dietrich, Special to the Journal
Freelance

At a time when the province’s biotech industry is fighting to establish a solid commercial biotech industry, its best hope for growth lies in the convergence of biotechnology with information technology, electronics and communications — some of Alberta’s strongest industries.

“It only makes sense that Alberta companies would work together to complement each other’s strengths,” said BioAlberta’s Myka Osinchuk.

“Since Alberta is so strong on the information and communications technology (ICT) side, we can begin to consider what the future opportunities are. There’s lots of potential there.”

Much of Alberta’s computing expertise comes from experience managing data for the energy sector, Osinchuk said. “Billions of bits of information are collected every year, and all of them are sorted and interpreted. Biotech researchers need to do this with their data.”

Project CyberCell, an initiative that recently began at the University of Alberta’s Institute for Biomolecular Design, promises to marry biotech research with information technology, engineering, physics, mathematics, bioinformatics, biophysics, chemistry and biochemistry.

Not only will the project involve researchers from many disciplines, but it will expand on current research being done in the areas of genomics and proteomics.

Genomics involves a complete description of all genes, their functions and organization, and the study of how this organization differs among individuals and species.

All genes contain functional instructions that are carried out by proteins. The study of the relationship of proteins to their functions is called proteomics.

Project CyberCell will look beyond the current “collection phase” of genomics and proteomics information, to examine the dynamic and structural nature of cellular processes at a quantitative level of chemical detail so that a living cell can be recreated computationally.

Essentially, the project aims to develop a “virtual” cell that can be manipulated at different levels of molecular resolution, and that can respond, adapt and evolve to fit its virtual environment.

E. coli will serve as the model that will generate the concepts and technology for extending the cybercell to more complicated cell types and eventually, multi-cellular organisms.

The marriage between bio and info technologies is critical to the success of CyberCell and other projects that involve large amounts of data management and computational analysis, says the director of the U of A’s Institute for Biomolecular Design and Project CyberCell.

“As biochemists we’re good at designing strategies to collect and interpret huge amounts of biological data,” said Mike Ellison, who is also a professor of biochemistry at the U of A.

“On the other hand, IT deals with managing, accessing and interrelating huge amounts of data. From my perspective, why reinvent the wheel?”

Renovations to the 8,000-sq-foot Institute for Biomolecular Research were completed last fall, with $13 million worth of equipment installed.

A multi-disciplinary team of researchers has begun to collect and organize data as the first step in Project CyberCell, Ellison said.

Although qualitative data have been collected by researchers worldwide, the data needed for CyberCell needs to be “quantitative and rigorous.”

“Once we have more funding in place, we’ll be working towards a full staff of about 130 people — principal investigators, graduate students, technicians and research associates.”

Ellison said researchers need to be able to test their predictions computationally, design computational strategies to get the cell to live on a computer, and then test the algorithms to see how closely the cell functions to a real cell.

Researchers eventually will use cybercells to test the potential effects of pesticides or pharmaceuticals on animal or human cells.

“The fear now with GMOs (genetically modified organisms) is that we don’t know what the long-term effects might be,” Ellison said. “But with a cybercell, we could add genetic information and see how it reacts. We’d be able to predict the real effects of rearranging or adding the genes based on what we found.”

Realistically, and “if all goes well,” it will take approximately 10 years to complete the E. coli cybercell, Ellison said. Between now and then, however, numerous intermediate discoveries will be able to be commercialized.

“The databases in and of themselves will be of value to researchers everywhere,” he said.

Even with some commercialization throughout the project, Ellison admits that funding such a mammoth undertaking is a challenge.

Eighty per cent of the funding received to date for the Institute has been devoted to CyberCell.

The other 20 per cent is devoted to providing platform technology support to other university research activities related to structural and functional proteomics.

The Institute has received $6 million from the Canada Foundation for Innovation, $4 million from the Alberta government’s Infrastructure and Intellectual Partnership Program, $4.5 million from the Alberta Science Research Authority, and $4 million from Western Economic Diversification. The U of A has also committed $5 million for new construction.

An application for an additional $22 million in infrastructure support for CyberCell will be made to the Canada Foundation for Innovation later this year. As well, Project CyberCell has been asked to resubmit its application for $50 million over five years to Genome Canada, the federal program set up to establish five world-class genome technology centres across the country.

Genome Canada: www.genomecanada.ca

ALBERTA BIOTECH

- At 44 per 1,000 population, Alberta has the highest number of engineers and researchers per capita in Canada.

- Alberta’s industry accounts for 7% of Canada’s biotech firms, generates 9% of the country’s biotech sales, Alberta’s research and development accounts for 8% of the national total and Alberta accounts for 10% of the country’s biotech employment.

- A growth of 50 biotech companies in Alberta over the next 10 years would have the following economic impact: new jobs in the range of 1,500 to 5,000, GDP increase of an amount in the range of $150 to $100 million.